PGS1

protein-coding

phosphatidylglycerophosphate synthase 1

Gene summary

Predicted to enable CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity and calcium ion binding activity. Predicted to be involved in cardiolipin biosynthetic process and diacylglycerol metabolic process. Located in endoplasmic reticulum. Is active in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_024419.5

Inheritance

—

ClinVar variants

U:90B:3

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr17:78,378,649-78,425,114

External References & Databases

Ensembl (ENSG00000087157)

Transcript & Mutation Effects

hg38 • Region Span ~46.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PGS1 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 84

Inborn genetic diseasesTotal: 13

not providedTotal: 5

DNAH17-related disorderTotal: 5

High myopiaTotal: 1

PGS1-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024419.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	2 clinvar		4
missense			85 clinvar	1 clinvar		86
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	90	3	0	93

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 86 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024419.5	RefSeq	NP_077733.3	9	MANE Select
ENST00000262764.11	Ensembl	ENSP00000262764.5	9	MANE Select
ENST00000586019.1	Ensembl	ENSP00000467569.1	2	Standard
ENST00000586355.1	Ensembl	ENSP00000467719.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glycerophospholipid metabolism - Homo sapiens (human)
Phospholipid Biosynthesis
Metabolism of lipids
cardiolipin biosynthesis
Metabolism

Biological Process

phosphatidylglycerol biosynthetic process
cardiolipin biosynthetic process
diacylglycerol metabolic process

Molecular Function

calcium ion binding
ATP binding
CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity

Cellular Component

mitochondrion
mitochondrial inner membrane
endoplasmic reticulum

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262764
Coding exons: 9
Length: 46475
Individuals with no LoFs: 124868
Homozygous LoFs: 0
Heterozygous LoFs: 50
Defined: 124918
p: 0.000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.50	254	331	0.768	0.0000211	3554
Missense (PolyPhen)		68	89.599	0.75894		864
Synonymous	-0.670	155	145	1.07	0.00000934	1178
Loss of Function	1.04	20	25.7	0.778	0.00000137	267

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0.00060	0.00060	rare
East Asian	0.00011	0.00011	rare
Finnish	0.00019	0.00019	rare
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.00026	0.00026	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Functions in the biosynthesis of the anionic phospholipids phosphatidylglycerol and cardiolipin. {ECO:0000250}.;

Recessive Scores

pRec: 0.130

Intolerance Scores

LoFtool: 0.361
RVIS EVS: -0.34
RVIS percentile EVS: 30.56

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.395

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium